USPS with Endicia you can batch create your shipping labels with an imported CSV.
If you aren't doing bulk mailing on the regular, USPS will be the lowest cost option.
UPS Mail Innovations, or FEDEX Smart Post, which USPS delivers to the end user may be able to cut some cost, but you don't know the rates all up front (Mail Innovations), and the time spent setting up the accounts with UPS / FedEx may surpass your savings on a 1000 shipments.
USPS is the cheapest option, unless you are regularly sending out 100+ small orders per day, then you can cut costs with the other services.